Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Vsx2

Cell type

Cell type Class
Neural
Cell type
Retina
MeSH Description
The ten-layered nervous tissue membrane of the eye. It is continuous with the OPTIC NERVE and receives images of external objects and transmits visual impulses to the brain. Its outer surface is in contact with the CHOROID and the inner surface with the VITREOUS BODY. The outer-most layer is pigmented, whereas the inner nine layers are transparent.

Attributes by original data submitter

Sample

source_name
Adult mouse retina
developmental stage
Adult
tissue
retina
strain
C57BL/6
chip antibody
VSX2 (Exalpha, Cat No. X1180P, Lot No 14166)
treatment
untreated

Sequenced DNA Library

library_name
GSM5860055
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Retinae were fixed, lysed and sheared to an average length of 300-500 bp. After incubation with antibody, beads were washed and DNA was extracted with phenol chroloform and precipitated with ethanol. Libraries were prepared according to Illumina's instructions

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
38479041
Reads aligned (%)
94.6
Duplicates removed (%)
27.6
Number of peaks
31415 (qval < 1E-05)

mm9

Number of total reads
38479041
Reads aligned (%)
94.5
Duplicates removed (%)
27.7
Number of peaks
31399 (qval < 1E-05)

Base call quality data from DBCLS SRA